Hi Anna,

  As Elaine says ChimeraX structure prediction is using ColabFold which is an optimized version of AlphaFold 2.  If you want the exact version of ColabFold and AlphaFold being used it is in the ChimeraX code

https://github.com/RBVI/ChimeraX/blob/f44f848ce802b3917680327e2383ab183195ffe2/src/bundles/alphafold/src/colabfold_predict.py#L226

and it is currently using something close to ColabFold 1.5.5 from Nov 2023

https://github.com/sokrypton/ColabFold/commit/29395e7dee2c2895eaf585ef6b6cde932fd95e72

which appears to use AlphaFold-ColabFold version 2.3.6 (seen in the ColabFold file)

https://github.com/sokrypton/ColabFold/blob/main/pyproject.toml

ColabFold uses a forked version of Google's AlphaFold project called AlphaFold-ColabFold

https://pypi.org/project/alphafold-colabfold/

So the exact versions used are a bit of trouble to track down.  At any rate it appears ChimeraX is using the most recent versions (but not AlphaFold 3).

Tom


On Aug 9, 2024, at 8:48 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Anna,
This is explained in the ChimeraX User Guide, see the help page for the AlphaFold tool -- you can press the "Help" button on that tool or see the copy at our website here:

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html>

To summarize,

(1) if you are using search or fetch, it is not running a new calculation but getting a pre-existing model from the AphaFold Database.

(2) if you are using predict to run a new prediction, it is using ColabFold which is an open-source optimized version of AlphaFold 2.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 9, 2024, at 3:19 AM, Anna Mestre Borras via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

I would like to confirm which is the AlphaFold version in ChimeraX 1.8 when using Tools --> structure prediction --> AlphaFold.

Thanks!
Best,
Anna


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